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Bioinformatics 2007 23(13):i433-i439; doi:10.1093/bioinformatics/btm169
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Polyploids, genome halving and phylogeny

David Sankoff 1,*, Chunfang Zheng 2 and Qian Zhu 3

1Department of Mathematics and Statistics, 2Department of Biology and 3Department of Biochemistry, University of Ottawa, Ottawa K1N 6N5, Canada

*To whom correspondence should be addressed.


  Abstract

Motivation: Autopolyploidization and allopolyploidization events multiply the number of chromosomes and genomic content. Genome rearrangement phylogenetics requires that all genomes analyzed have the same set of orthologs, so that it is not possible to include diploid and polyploid genomes in the same phylogeny.

Results: We propose a framework for solving this difficulty by integrating the rearrangement median and genome halving algorithms. Though the framework is general, some problems remain open. We implement a heuristic solution to the prototypical case of a tree with one tetraploid and two diploid genomes, and apply it to study the evolution of cereals and of yeast.

Contact: sankoff{at}uottawa.ca


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C. Zheng, Q. Zhu, Z. Adam, and D. Sankoff
Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes
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[Abstract] [PDF]


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